8QRE | pdb_00008qre

Cholera holotoxin (wildtype)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8QRE

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Using Vibrio natriegens for High-Yield Production of Challenging Expression Targets and for Protein Perdeuteration.

Mojica, N.Kersten, F.Montserrat-Canals, M.Huhn Iii, G.R.Tislevoll, A.M.Cordara, G.Teter, K.Krengel, U.

(2024) Biochemistry 63: 587-598

  • DOI: https://doi.org/10.1021/acs.biochem.3c00612
  • Primary Citation Related Structures: 
    8QRE

  • PubMed Abstract: 

    Production of soluble proteins is essential for structure/function studies; however, this usually requires milligram amounts of protein, which can be difficult to obtain with traditional expression systems. Recently, the Gram-negative bacterium Vibrio natriegens emerged as a novel and alternative host platform for production of proteins in high yields. Here, we used a commercial strain derived from V. natriegens (Vmax X2) to produce soluble bacterial and fungal proteins in milligram scale, which we struggled to achieve in Escherichia coli . These proteins include the cholera toxin (CT) and N -acetyl glucosamine-binding protein A (GbpA) from Vibrio cholerae , the heat-labile enterotoxin (LT) from E. coli and the fungal nematotoxin CCTX2 from Coprinopsis cinerea . CT, GbpA, and LT are secreted by the Type II secretion system in their natural hosts. When these three proteins were produced in Vmax, they were also secreted and could be recovered from the growth media. This simplified the downstream purification procedure and resulted in considerably higher protein yields compared to production in E. coli (6- to 26-fold increase). We also tested Vmax for protein perdeuteration using deuterated minimal media with deuterium oxide as solvent and achieved a 3-fold increase in yield compared to the equivalent protocol in E. coli . This is good news, since isotopic labeling is expensive and often ineffective but represents a necessary prerequisite for some structural biology techniques. Thus, Vmax represents a promising host for production of challenging expression targets and for protein perdeuteration in amounts suitable for structural biology studies.


  • Organizational Affiliation
    • Department of Chemistry, University of Oslo, NO-0315 Blindern, Oslo, Norway.

Macromolecule Content 

  • Total Structure Weight: 174.34 kDa 
  • Atom Count: 13,002 
  • Modeled Residue Count: 1,498 
  • Deposited Residue Count: 1,510 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit AA,
G [auth B]
240Vibrio cholerae O1Mutation(s): 0 
Gene Names: ctxA
UniProt
Find proteins for P01555 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01555 
Go to UniProtKB:  P01555
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01555
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit B103Vibrio cholerae O1Mutation(s): 2 
Gene Names: ctxBtoxBVC_1456
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01556
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLA

Query on GLA



Download:Ideal Coordinates CCD File
IA [auth C]alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
GAL

Query on GAL



Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth H]
KA [auth I]
N [auth A]
NA [auth J]
AA [auth G],
CA [auth H],
KA [auth I],
N [auth A],
NA [auth J],
PA [auth K],
QA [auth L],
S [auth D],
U [auth E],
X [auth F]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
Y [auth G]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth G]
DA [auth H]
GA [auth B]
JA [auth C]
LA [auth I]
BA [auth G],
DA [auth H],
GA [auth B],
JA [auth C],
LA [auth I],
MA [auth I],
O [auth A],
OA [auth J],
P [auth A],
Q [auth A],
RA [auth L],
SA [auth L],
T [auth D],
V [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
HA [auth C],
W [auth F],
Z [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
EA [auth B],
FA [auth B],
M [auth A],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.659α = 90
b = 108.128β = 95.958
c = 124.765γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03AI112854
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI137056

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary